How to set the origin of sub-meshes without it affecting the armature?
Place the model and armature in the center of the scene with both origins at 0,0,0. Then you won't have to re-set origins every time but scaling the model and applying the scale will always affect rigging. There is no way around it except scaling rig to which the model is parented, you probably want to avoid it though, if you want to export model with animations to some other environment, like Unity or Unreal. The best solution to this problem would be to rig the model after all mesh changes are finished.